{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001303","ANALYSIS_ID":"AN002171","VERSION":"1","CREATED_ON":"January 9, 2020, 1:15 pm"},

"PROJECT":{"PROJECT_TITLE":"TGFβ3 heterozygous mice","PROJECT_TYPE":"Mice nephropathy in lipotoxic model","PROJECT_SUMMARY":"Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.","INSTITUTE":"University Rey Juan Carlos","DEPARTMENT":"Basics Science of Health","LAST_NAME":"Lanzon","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain","EMAIL":"borja.lanzon@urjc.es","PHONE":"663692554"},

"STUDY":{"STUDY_TITLE":"TGF-Beta 3 heterozygous mice","STUDY_TYPE":"Mice nephropathy in lipotoxic model","STUDY_SUMMARY":"Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.","INSTITUTE":"University Rey Juan Carlos","DEPARTMENT":"Basics Science of Health","LAST_NAME":"Lanzon","FIRST_NAME":"Borja","ADDRESS":"Avenida de Atenas S/N","EMAIL":"borja.lanzon@urjc.es","PHONE":"663692554","NUM_GROUPS":"2","TOTAL_SUBJECTS":"14","NUM_MALES":"14"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"c57bl6","AGE_OR_AGE_RANGE":"16 weeks","GENDER":"Male"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"269 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 269"}
},
{
"Subject ID":"-",
"Sample ID":"119 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 119"}
},
{
"Subject ID":"-",
"Sample ID":"267 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 267"}
},
{
"Subject ID":"-",
"Sample ID":"130 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 130"}
},
{
"Subject ID":"-",
"Sample ID":"127 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 127"}
},
{
"Subject ID":"-",
"Sample ID":"98 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 98"}
},
{
"Subject ID":"-",
"Sample ID":"25 HZCD",
"Factors":{"Genotype":"HZCD"},
"Additional sample data":{"RAW_FILE_NAME":"HZ-CD 25"}
},
{
"Subject ID":"-",
"Sample ID":"132 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 132"}
},
{
"Subject ID":"-",
"Sample ID":"251 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 251"}
},
{
"Subject ID":"-",
"Sample ID":"120 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 120"}
},
{
"Subject ID":"-",
"Sample ID":"79 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 79"}
},
{
"Subject ID":"-",
"Sample ID":"129 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 129"}
},
{
"Subject ID":"-",
"Sample ID":"128 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 128"}
},
{
"Subject ID":"-",
"Sample ID":"92 WTCD",
"Factors":{"Genotype":"WTCD"},
"Additional sample data":{"RAW_FILE_NAME":"WT-CD 92"}
},
{
"Subject ID":"-",
"Sample ID":"QC1",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC1"}
},
{
"Subject ID":"-",
"Sample ID":"QC2",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC2"}
},
{
"Subject ID":"-",
"Sample ID":"QC3",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC3"}
},
{
"Subject ID":"-",
"Sample ID":"QC4",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC4"}
},
{
"Subject ID":"-",
"Sample ID":"QC5",
"Factors":{"Genotype":"QC"},
"Additional sample data":{"RAW_FILE_NAME":"QC5"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Kidney samples were powdered with mortar and pestle. Method used for extraction was previously validated for tissue","SAMPLE_TYPE":"Kidney","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Kidney homogenate was prepared by adding cold (−20 °C) methanol/water (1:1, v/v), (1:10 tissue/solvent). Tissue disruption was achieved with Tissue- Lyser LT homogenizer (Qiagen, Germany) for metabolite extraction."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"100 μL of kidney tissue homogenate was vortex-mixed with 320 μL of methanol for 2 min, followed by the addition of 80 μL of MTBE for the extraction of nonpolar compounds. Then, vials were rapidly capped and placed on a shaker for 1 h at room temperature. The extracted samples were centrifuged at 4000g for 20 min at 20 °C. For GC−MS analysis, 300 μL of supernatant was evaporated to dryness (SpeedVac Concentrator System, Thermo Fisher Scientific, Waltham, MA). Methoxymation was then performed with 20 μL of O-methoxyamine hydrochloride (15 mg/mL in pyridine) and vigorously vortex-mixed for 5 min. Vials were then incubated in darkness at room temperature for 16 h. For silylation, 20 μL of BSTFA/TMCS (99:1) was added and vortex-mixed for 5 min, and capped vials were placed in the oven at 70 °C for 1 h. Finally, 100 μL of heptane containing tricosane (20 ppm) as internal standard (IS) was added to each vial prior to injection. For LC−MS analysis, 90 μL of supernatant was transferred to an ultra-high-performance liquid chromatography−mass spectrometry.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"GC-MS","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890B","COLUMN_NAME":"Agilent DB5-MS (30m x 0.25mm, 0.25um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 7890A","INSTRUMENT_TYPE":"GC QTOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"An Agilent GC instrument (7890A) coupled to an inert mass spectrometer with triple-Axis detector (5975C, Agilent Technologies) was used for kidney tissue fingerprinting. Briefly, 1 μL of derivatized samples were injected by an Agilent autosampler (7693). Samples were automatically injected in split mode (split ratio 1:12), into an Agilent ultra-inert deactivated glass wool split liner. Compound separation was achieved using a pre-column (10 m J&W integrated with Agilent 122-5532G) combined with a GC column DB5-MS (length, 30m; inner diameter, 0.25 mm; and 0.25 μm film of 95% dimethyl/5% diphenylpolysiloxane). The flow rate of helium carrier gas was constant at : 0.938 mL/min through the column. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 minutes was performed. The column oven temperature was initially set at 60°C (maintained for 1 minute), then raised by 10°C/min until it reached 325°C, and then was held at this temperature for 10 minutes before cooling down. The injector and the transfer line temperatures were established at 250°C and 280°C, respectively. MS system: the electron impact ionization operating parameters were set as follows: filament source temperature, 230°C; electron ionization energy, 70 eV. Mass spectra were collected over a mass range of 50-600 m/z at a scan rate of 10 spectra/s. Data were acquired using the Agilent MSD ChemStation Software (Agilent Technologies). For retention index determination, a mixture of n-alkanes (C8-C28) dissolved in nhexane was run prior to the samples. Data were acquired using Agilent MSD ChemStation Software (Agilent Technologies).","MS_RESULTS_FILE":"ST001303_AN002171_Results.txt UNITS:Area Has m/z:Neutral masses Has RT:Yes RT units:Minutes"}

}